Mercurial > repos > ebi-gxa > retrieve_scxa
changeset 1:cc21614b6693 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 7bf75360bdf687f987e706c3e48667931eaed0ce-dirty
| author | ebi-gxa |
|---|---|
| date | Tue, 13 Aug 2019 05:36:12 -0400 |
| parents | cd6b80f62fcc |
| children | 72b6e1747e37 |
| files | retrieve-scxa.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/retrieve-scxa.xml Wed Apr 03 12:01:53 2019 -0400 +++ b/retrieve-scxa.xml Tue Aug 13 05:36:12 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.1+galaxy1"> +<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2"> <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description> <requirements> - <requirement type="package" version="1.18">gnu-wget</requirement> + <requirement type="package" version="1.20.1">wget</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -19,8 +19,8 @@ wget -O ${matrix_mtx} 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx'; wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_cols' | cut -f2 > ${barcode_tsv}; -wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_rows' - | awk '{OFS="\t"; print \$2,\$2}' > ${genes_tsv}; +wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.decorated.mtx_rows' | + awk -F'\t' '{ if (length($2) == 0) { print $1"\t"$1 } else { print $0 } }' > ${genes_tsv}; #end if @@ -88,6 +88,7 @@ already normalized/scaled. You should keep this in mind when using this data on methods that will try to normalise data as part of their procedure. Due to technical particularities in the current Atlas SC pipeline, TPMs available here are not filtered. + **Note: droplet databases won't have TPM data** Outputs will be: